Заявку на участие отправлять до 15 апреля Вячеславу Иваненко ivanenko.slava@gmail.com т.9153201967
Two-day course at Moscow State Univ
Molecular phylogenies to answer ecological questions
Diego Fontaneto
www.cnr.it/people/diego.
https://scholar.google.ru/
Defining units of diversity, disentangling the evolutionary history of a species, assessing the phylogenetic structure of communities are all pressing questions in ecology. Molecular phylogenies represent a pivotal help in unravelling them.
The two-day course will be devoted to: (1) providing a brief overview of the phylogenetic methods and software to obtain molecular phylogenies from DNA sequence data; (2) outlining the use the phylogenies as a base for DNA taxonomy.
During the course, students will be exposed to different ideas, rationale, methods, tools, and software that will widen their toolkit for their own research activities. Great emphasis will be placed on the use of the statistical software R to handle data and to perform specific statistical tests. All software used for the course is free and can be downloaded from the web.
Maximum number of participants: 10
Program
May 12th, overview of phylogenetic methods
morning, 2 hours lecture
- introduction on the use of phylogenies in ecology,
- phylogenetic methods (distance, parsimony, maximim likelihood, bayesian) and their rationale,
- the steps for a phylogenetic reconstruction: alignment, evolutionary model selection, analysis, visualisation, afternoon, 3 hours practice, each one with its own laptop (or in a computer room), with these softwares installed (all freely available online)
- modelgenerator, https://bioinf.nuim.ie/
modelgenerator/ - R (package ape), https://www.r-project.org/
- PhyML, https://www.atgc-montpellier.
fr/phyml/versions.php - MrBayes, https://mrbayes.sourceforge.
net/download.php - BEAST (including BEAUti, Tracer, TreeAnnotator, and TreeView), https://beast.bio.ed.ac.uk/
software/ and connected online to use other methods remotely
May 13th, methods in DNA taxonomy morning, 2 hours lecture
- DNA taxonomy (how to use phylogenies to identify and delimit species)
afternoon, 3 hours practice, each one with its own laptop (or in a computer room), with these softwares installed (all freely available online)
- R (package ape, splits)
- and connected online to use other methods remotely
